A depth of submucosal invasion (DSI) of ≥1000 μm is an important risk factor for lymph node metastasis (LNM) in patients with submucosal invasive (pT1) colorectal cancer (CRC), according to the European Society of Gastrointestinal Endoscopy and the Japanese Society for Cancer of the Colon and Rectum (JSCCR) guidelines. According to the latter, if the location of the muscularis mucosae in the invasive area is not confirmed, the DSI can be measured from the surface. In these cases, a 'remaining intramucosal lesion' (rIL), which is in the invasive area, is sometimes observed. To avoid over-measuring the DSI, we proposed a 'modified DSI' (mDSI), which excludes the rIL from the JSCCR DSI. We investigated the characteristics and effectiveness of the rIL and mDSI by grouping cases with polypoid growth (PG) and non-polypoid growth (NPG) histologically. Three hundred and thirty-nine consecutive patients with pT1 CRC were examined. LNM was detected in 37 cases. The distribution of the DSI and rIL was significantly higher in PG than in NPG cases (P<0.001). There was no difference in the mDSI distribution between the PG-/NPG-type cases. An rIL was observed in 39% (127/301) of cases, in which the location of the muscularis mucosae could not be determined or estimated and the mDIS could be estimated. In 13% (16/127) of cases, the mDSI was effective (JSCCR DSI ≥1000 and mDSI <1000 μm). Among these 16 cases, 11 (69%) did not have risk factors (mDSI, lymphovascular invasion, budding grade, or special histological types) and may have avoided unnecessary surgery.